An m68060 card would obviously have its own ROM to initialize things on boot. From a userland perspective, the instruction set is identical. The only program that I remember having trouble with the m68060 with all of the features enabled was Adobe Illustrator, so I'd have to switch off superscalar mode before running that.

The m68060 running Mac OS was definitely faster than the first generation of PowerPC 601 systems. Part of the issue, I'm sure, was the fact that m68060s might slow adoption of PowerPC, but another (and altogether important) reason was the cost. As you can see from the numbers, it'd cost almost as much for an m68060 accelerator as it would for a new machine. PowerPC accelerators for m68k Macs certainly didn't cost that much.